Gallus gallus Data at NCBI: From Genome Annotation to Gene Curation

The National Center for Biotechnology Information (NCBI) reference sequence (RefSeq) project provides several resources to support the chicken research community. These include: genome annotation; evidence-based transcript and protein sequence records; BLAST databases; annotation reports; FTP data; and entries in NCBI’s Gene resource. Gene, transcript, and protein data are provided using a combined approach of targeted manual curation, collaboration with the AgBase and the Chicken Gene Nomenclature Committee (CGNC), and whole genome annotation by NCBI’s eukaryotic genome annotation pipeline. The eukaryotic genome annotation pipeline uses the available known RefSeqs (NM_, NR_, and NP_ accessions that have curation support), RNA-Seq, cDNA/EST/TSA, and protein alignments to generate whole genome annotation and corresponding model RefSeq RNA and protein sequence products (XM_, XR_, XP_ accessions).  Manual curation focuses on both sequence and gene data. For example, in 2015 curators reviewed putative sequence errors (such as frameshifts), removing redundant gene and ortholog data, and nomenclature conflicts affecting paralogs,  gene families, or between NCBI’s Gene database and CGNC. The presentation will present genome annotation results for the current public version of the chicken assembly, examples of RefSeq curation, and information on data access. More information about NCBI’s RefSeq project is available from: www.ncbi.nlm.nih.gov/refseq/